# Package picard.sam.markduplicates

package picard.sam.markduplicates

Related Packages
Package
Description
picard.sam
picard.sam.markduplicates.util
picard.sam.SamErrorMetric
picard.sam.util
Class
Description
CheckDuplicateMarking
CheckDuplicateMarking.Mode
CollectDuplicateMetrics
Collect DuplicateMark'ing metrics from an input file that was already Duplicate-Marked.
EstimateLibraryComplexity
Attempts to estimate library complexity from sequence alone.
MarkDuplicates
A better duplication marking algorithm that handles all cases including clipped and gapped alignments.
MarkDuplicates.DuplicateTaggingPolicy
Enum used to control how duplicates are flagged in the DT optional tag on each read.
MarkDuplicates.DuplicateType
Enum for the possible values that a duplicate read can be tagged with in the DT attribute.
MarkDuplicatesForFlowArgumentCollection
MarkDuplicatesForFlowHelper
MarkDuplicates calculation helper class for flow based mode The class extends the behavior of MarkDuplicates which contains the complete code for the non-flow based mode.
MarkDuplicatesHelper
MarkDuplicatesWithMateCigar
An even better duplication marking algorithm that handles all cases including clipped and gapped alignments.
MarkDuplicatesWithMateCigarIterator
This will iterate through a coordinate sorted SAM file (iterator) and either mark or remove duplicates as appropriate.
SimpleMarkDuplicatesWithMateCigar
This is a simple tool to mark duplicates using the DuplicateSetIterator, DuplicateSet, and SAMRecordDuplicateComparator.
UmiAwareMarkDuplicatesWithMateCigar
This tool locates and tags duplicate reads in a BAM or SAM file, where duplicate reads are defined as originating from a single fragment of DNA.
UmiGraph
UmiGraph is used to identify UMIs that come from the same original source molecule.
UmiMetrics
Metrics that are calculated during the process of marking duplicates within a stream of SAMRecords using the UmiAwareDuplicateSetIterator.